I means that 96% of the fuel is being injected BTDC, and 4% after. The calculator takes actual injection duration (uses rpms, volume, pressure, and duration table) and crank degrees per us to calculate it. So you put 50 in the calculator it will look at the rpms, then the desired quantity of fuel, and the commanded pressure, using those numbers it looks at the duration table to determine how long the pulse needs to be. Let's says it's a 1000us pulse, and you are at 3000 rpms. At 3000 rpms each degree of crank rotation takes 55.6us. So 1000/55.6 is 18.0 which means the injector will be open for 18.0 degrees. Since you have 50 in the calc that means 50% before, a direct split, so the timing table would read 9.0. If you had 100 it would read 18.0, 150 would read 27.0, -100 would read -18.0, -150 would read -27.0, or 96 would read 17.3.
150% means that the injection will start 150% BTDC based on time, so on a 1000us pulse it would start 1500us BTDC which at 55.6 us/deg is 27.0 deg of timing.
Does the make sense?